Abstract: Field investigation was carried out in 2016 and 2017, indexes including seawater, sediment, seagrass, plankton, zoobenthos and benthic macroalgae was obtained from Liusha bay of Guangdong Province.The results showed that average biomass and total distribution area of Halophila ovalis were 3.74 g/m² and 26.9 hm² with patches distribution pattern.Three habitat types were divided by principal component-cluster analysis of seawater parameters, they were "influence area of fish raft and fishing net" (Area Ⅰ), "shellfish farming area" (Area Ⅱ) and "non-cultured area" (Area Ⅲ).Comprehensive scores of principal component showed that Area Ⅰ was most polluted.Comparison between Area Ⅰ and Area Ⅱ showed that biomass of seagrass and zoobenthos, concentration of dissolved oxygen and active phosphate, phytoplankton abundance, salinity in Area Ⅰ were lower than that in Area Ⅱ, biomass of benthic macroalgae, N/P ratio, concentration of ammonia nitrogen, inorganic nitrogen and COD in Area Ⅰ were higher than that in Area Ⅱ.Total distribution area and biomass of seagrass bed in Liusha bay seriously degraded in 2017 when compared with that in 2002.Due to the production mode of fish raft and fishing net, mass multiplication of small shellfishes and low-salinity water derived from river input, seagrass biomass decreased.The relationship between seagrass biomass and other indexes reflected that shellfish culture played a positive role in seagrass survival and strong self-purifying ability of water was beneficial to seagrass growth.Also, this paper put forward the suggestions of protecting seagrass including promoting public consciousness, strengthening natural reserve management and implementating normal monitoring.